I lecture Biochemistry at a small University in Oporto. Although originally raised as an experimental Biochemist, I have since changed my research into theoretical and computational chemistry and biochemistry. In this blog, I will mostly commment on recent (or not so recent...) research papers that happen to have called my attention. I hope someone will find it interesting/useful :-)

Monday, September 8, 2014

My most recent paper has just been published in PeerJ . It was a LONG time in the making, to the point that my 12-yo daughter once told me (only half-in-jest), that I should "cut my losses and forget about it". I am quite happy about how it turned out: besides describing an analysis of a reaction mechanism and the influence of the redox state of a hard-to-converge Fe-S cluster , it also contains the first computations including the weighed contributions of 1.2*1013 protonations states of a protein on the reaction it catalyzes. The computational approach described here is relatively simple to perform provided that one has a good estimate of the relative abundances of those protonation states, which can be obtained through Monte Carlosampling once the site-site interactions have been computed with a Poisson-Boltzmann solver. To my mind, this is clearly superior to the usual approach of considering only the "most likely" protonation state (which may often not be the state with the most significant influence on the electrostatic field surrounding the active site). What do you think of it?